In patients treated with chemotherapy and bone marrow transplantation for leukemia, there are variable rates of reconstitution of T cell numbers and function. An understanding of the mechanisms underlying the recovery of T cells will be important for the design of future strategies to improve T cell reconstitution. The thymus is the organ responsible for producing new naive T cells with a broad immune repertoire from bone marrow-derived precursors. This study examines the role of the thymus in immune reconstitution and how it is affected by immunosuppression and graft-versus-host disease. We also pursue the same therapeutic goals in HIV-infected individuals aiming to improve immune reconstitution. In patients treated with chemotherapy and bone marrow transplantation for leukemia, there are variable rates of reconstitution of T cell numbers and function. An understanding of the mechanisms underlying the recovery of T cells will be important for the design of future strategies to improve T cell reconstitution. The thymus is the organ responsible for producing new naive T cells with a broad immune repertoire from bone marrow-derived precursors. This study examines the role of the thymus in immune reconstitution and how it is affected by immunosuppression and graft-versus-host disease. We also pursue the same therapeutic goals in HIV-infected individuals aiming to improve immune reconstitution.